recipe pyrovelocity

Probabilistic RNA velocity for cell fate uncertainty estimation

Homepage:

https://github.com/pinellolab/pyrovelocity

Documentation:

https://pyrovelocity.readthedocs.io/en/latest/

License:

GPL / Affero GPL V3

Recipe:

/pyrovelocity/meta.yaml

package pyrovelocity

versions:

0.1.0-1,  0.1.0-0

depends adjusttext:

depends anndata:

0.7.5

depends astropy:

depends h5py:

depends ipykernel:

depends ipywidgets:

depends jupyterlab:

depends pyro-ppl:

1.6.0

depends python:

3.8.8

depends pytorch-gpu:

1.8.*

depends pytorch-lightning:

1.3.0

depends scvelo:

0.2.4

depends scvi-tools:

0.13.0

depends seaborn:

0.11.2

depends torchmetrics:

0.5.1

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install pyrovelocity

and update with::

   mamba update pyrovelocity

To create a new environment, run:

mamba create --name myenvname pyrovelocity

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/pyrovelocity:<tag>

(see `pyrovelocity/tags`_ for valid values for ``<tag>``)

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